When William Boyd adapted Scoop, Evelyn Waugh's great comic novel, he left out one of its best jokes. The book's innocent hero, William Boot, writes Lush Places, the Daily Beast's nature column. But his copy is mangled by his minx of a sister. Whenever the word "badger" appears, Priscilla replaces it with "great crested grebe" before sending off the article, making the thing absurd and provoking derisive letters. "A major in Wales," wrote Waugh, "challenged him categorically to produce a single authenticated case of a great crested grebe attacking young rabbits."

Boyd couldn't make Waugh's joke work on film. Succinct on paper, it would have been a celluloid clunker, requiring a close up of Boot's badger article held long enough to get the gist of the piece. Then a shot of Priscilla crossing out "badger" and writing "great crested grebe". Then a shot of the printed version about the newly libelled bird. No matter - when Scoop was broadcast there was a furore. How could Boyd have been so crass as to leave the joke out?

That reaction still piques Boyd as we sit in his Chelsea living room filled with beautiful books, many his own, not one paperback, even though the film was screened 19 years ago. "To judge a film by the book it's based on is very harsh," he says. "Nobody goes to see Verdi's Falstaff and goes home and reads The Merry Wives of Windsor. Nobody berates Verdi for leaving out so much of the play. And that should apply to film as well. When you adapt a book for film, you lose 60 or 70% of it."

But there is a more fundamental problem with screen adaptations that Boyd has run into repeatedly in a quarter of a century of writing screenplays. All the playful storytelling devices that the novelist can deploy are obliterated in film. "You're hampered by the medium," says Boyd. "Take the adaptation of my first novel, A Good Man in Africa. The novel is told entirely from the point of view of the central character. The film doesn't reproduce that exclusive, subjective point of view, because you're shooting it from an objective point of view, the camera lens, even if you have - as we did - a voiceover."

William Boyd is one of the few leading British novelists to be professionally bothered about these issues. Of the generation that spawned Amis, Barnes, McEwan and Ishiguro (he was selected in 1983 as one of Granta's 20 best young British novelists), Boyd, 53, is the only one to have another career writing screenplays. Since his first novel appeared in 1981 while he was a junior English don at Oxford, he has written eight more novels and two short story collections, but also adapted his own books, including Stars and Bars and Armadillo, those of others (including Mario Vargas Llosa's Aunt Julia and the Scriptwriter), original screenplays (he has a low-budget thriller in his drawer) and purported historical incidents. He is currently working with director Fred Schepisi on a Vietnam film called Last Man, about Australian special forces troops stuck behind enemy lines.

Boyd once mused whether choosing to write screenplays rather than journalism had made him less fashionable than his peers. If literary fashion was measured by gongs - which it isn't - Boyd would be in vogue, having received a CBE last year. Of screenwriting, he says: "It's a totally different beast from writing a novel. The cinema is a world of constraints and parameters and barriers, while the world of writing a novel is freedom."

It sounds a royal pain. Why do it? "Partly because when you finish a novel the tank is empty and you need to fill it up again. Also I use my film writing as a way of getting out of the house and meeting people. I've got more friends who are actors, producers and directors than writers."

Are any novels unfilmable? "Yes. Ulysses is pretty unfilmable, but that hasn't stopped people trying. Lolita is unfilmable but has been filmed twice. Nabokov wrote a screenplay for it that Kubrick threw out." Nevertheless, Boyd quotes approvingly Nabokov's dictum that films should be "vivacious variants" of the original.

There is an abject history of unrealised screenplays that would have yielded better films than the schlock that gets made. Boyd has a little library of the ones he loves upstairs. Among them is Harold Pinter's unfilmed screenplay of the biggest novel ever written, Proust's A La Recherche du Temps Perdu. He adores, too, Shane Black's script for the Bruce Willis picture, The Last Boy Scout - "a much better script than the film". Boyd also mentions the thwarted adaptation of a book by Pinter's wife, the historian Antonia Fraser, that he wrote for Universal in the late 90s. "It's based on her wonderful book about the Gunpowder Plot. I wrote the script, we had a director attached, it was moving forward and then there was one of those nights of the long knives at Universal Studios. Everybody got fired, and with them went their projects. "It was probably a symbolic end of an era because I don't think you would get through the door for a project about the Gunpowder Plot today." Why not? "Because it's 1605, men in tights and nobody's heard of it."

Last year the BBC asked him to write a screenplay to dramatise the love triangle of Shakespeare's sonnets - the dark lady, the fair youth and the Bard who fancied them both. The script was thus to be a free adaptation of Shakespeare's life, involving all the creative licence that he brought to adapting novels, and likely to provoke more literary outrage. Boyd readily agreed to make the drama none the less, calling it A Waste of Shame (after sonnet 129 "Th'expense of spirit in a waste of shame / Is lust in action"), and identifying the fair youth as William Herbert, the hotsy-totsy young Earl of Pembroke, and the dark lady as a Southwark strumpet called Lucie. Where Tom Stoppard's script for Shakespeare in Love had the Bard as a randy hetero, Boyd's more plausible account has him as a troubled bisexual who fails to consummate his lust for the fair youth but contracts the pox from the dark lady, and has to take a mercury bath cure as a result. "The circumstantial evidence seemed to me to be overwhelming and, if you're a writer of fiction, all you need is circumstantial evidence. If you're a scholar or historian you need more, but I can go where scholars and historians would not dare to tread."

But the identities of the dark lady and the fair youth have been academically incendiary matters ever since 1889. In that year, in Tite Street, just around the corner from Boyd's Chelsea home, Oscar Wilde wrote a short story called The Portrait of Mr WH that contended the fair youth to whom Shakespeare was homoerotically drawn was an actor called Willie Hews. Others later argued the youth was the Earl of Southampton, who may have been hotsy-totsy, but was not so young as the Earl of Pembroke. Boyd says this is unlikely: "Anthony Burgess wrote a fantastic novel about this called Nothing Like the Sun, but he identifies Southampton as the young man in the sonnets and it caused him terrible problems narratively because everything that happens to him has to happen earlier. So Shakespeare is a very young man and it just doesn't ring true. He can't even deal with the writing of Hamlet because everything is happening in the 1580s, or the 1570s even. The bitterness and world-weariness and sagacity of the sonnets seem to me to indicate someone who has lived a lot, not somebody who is 22."

Who was the dark lady? AL Rowse once wrote: "I have found her!" and identified the woman as an aristocrat called Emilia Lanier, but Boyd finds this implausible. He was convinced by the arguments of Katherine Duncan-Jones, historical adviser on his BBC film, that it was impossible for a man like Shakespeare to have the kind of sexual relationship described in the sonnets with an aristocrat. "The class gulf was too wide. But he was a successful man a long way from his estranged wife in Stratford. So it's entirely feasible that he saw prostitutes. So I thought let's make her a North African, Moorish, francophone hooker."

Even Duncan-Jones won't go that far. "She argues that the dark lady is a stereotype, not a real person, but there is no way when you are writing for fiction that you can have a stereotype." The nature of the medium, then, impelled Boyd to the creative licence he would never have contemplated as an academic.

On Monday, Boyd will defend the programme at the Royal Society of Literature. Isn't he afraid of getting lynched by seething Shakespeareans? "We'll see. You open a can of worms when you write about this because there are so many cranky theories out there." Including your own? For the first and last time during the interview, Boyd gets donnish: "I can be audacious, but everything I suggest is backed up by textual evidence." Boyd and the Bard, a Royal Society of Literature discussion, is on Monday. Details at www.rslit.org. His second world war novel, Restless, will be published by Bloomsbury in September